Genomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume

Abstract

For species with potential as new crops, rapid improvement may be facilitated by new genomic methods. Apios (Apios americana Medik.), once a staple food source of Native American Indians, produces protein-rich tubers, tolerates a wide range of soils, and symbiotically fixes nitrogen. We report the first high-quality de novo transcriptome assembly, an expression atlas, and a set of 58,154 SNP and 39,609 gene expression markers (GEMs) for characterization of a breeding collection. Both SNPs and GEMs identify six genotypic clusters in the collection. Transcripts mapped to the Phaseolus vulgaris genome–another phaseoloid legume with the same chromosome number–provide provisional genetic locations for 46,852 SNPs. Linkage disequilibrium decays within 10 kb (based on the provisional genetic locations), consistent with outcrossing reproduction. SNPs and GEMs identify more than 21 marker-trait associations for at least 11 traits. This study demonstrates a holistic approach for mining plant collections to accelerate crop improvement.

De Novo Domestication: An Alternative Route toward New Crops for the Future

“…Examples of this approach include the shatter-proofing of weeping rice grass (Microlaena stipoides), an Australian wild relative of rice, via mutagenesis of the orthologs of qSH1 and sh4 genes (Shapter et al, 2013), while crop productivity in tomato has been improved by combining induced mutations in the florigen pathway (Park et al, 2014). Furthermore, a number of genome-sequencing studies have been initiated for species that can be regarded as currently in the process of being domesticated, including intermediate wheatgrass (Thinopyrum intermedium), field pennycress (Thlaspi arvense), tree tobacco (Nicotiana glauca), and apiois (Apiose americana) (Dorn et al, 2015;Belamkar et al, 2016;Kantarski et al, 2017;Usadel et al, 2018). These studies provide clear proof of principle that the alteration of single domestication genes can dramatically improve the potential of little-or non-cultivated species.…”

“…As such, its use is currently largely restricted to cases wherein a loss-of-function mutation will lead to the domestication phenotype. That said, the number of species whose genomes have been edited is rapidly expanding (Osterberg et al, 2017), and important examples of loss-offunction mutants with beneficial effects include those enhancing rice and maize yields (Belamkar et al, 2016;Shi et al, 2017), the generation of virus-resistant cucumber (Chandrasekaran et al, 2016) and mildew-resistant wheat , improved soybean oil content (Haun et al, 2014), and potato storage ability (Clasen et al, 2016), as well as potentiating rubber production in dandelion (Iaffaidano et al, 2016).…”

Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height

“…DNA samples extracted were used for SNP genotyping using the SoySNP660K BeadChip at Beijing Boao Biotechnology Co., Ltd. A total of 54836 SNPs across 20 chromosomes remained after quality filtering; SNP markers were excluded by minor allele frequency (MAF < 0.05), and the maximum missing sites per SNP was <10% (Belamkar et al, 2016). These SNPs were used for analysis of population structure and GWAS.…”

A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes

“…Molecular markers and genetic maps have been crucial in genetic diversity analysis and in speeding up the breeding efforts in many crops (Staub et al 1996 ; Xu and Crouch 2008 ; Dhillon et al 2009 ; Roy et al 2011 ; Jiang 2013 ; Belamkar et al 2016 ). The recombination-based ordering of molecular markers can help in dissecting genotype–phenotype relationships and in map-based cloning.…”

“…Both diploid (2 n = 2 x = 22) and triploid (3 n = 3 x = 33) forms exist for apios (Seabrook and Dionne 1976 ). Apios has a haploid genome size of ~ 830 Mbp (Bai et al 2012 ; Belamkar et al 2016 ). Triploid populations are evidently sterile (Bruneau and Anderson 1988 ) and propagate through vegetative means.…”